Transcoding - sometimes slow, sometimes fast and sometimes not at all?

This is odd...Sometimes Encore CS5.5 will transcode fast, sometimes slow and sometimes it would't transcode at all. (No errors. Seems like the program stop and go to sleep) And this is on the same project without any changes. I just tried to restart my PC, restart Encore several times, and everytime It wil behave differently. Why?

These may, or may not, help... but free to read...
Odd Errors http://forums.adobe.com/thread/670174
Long File Names or odd characters cause problems
Read http://forums.adobe.com/thread/588273
And #4 http://forums.adobe.com/thread/666558
And This Message Thread http://forums.adobe.com/thread/665641
Also, make sure you do not have even a 1 frame gap between video files

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